Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

The color still indicates the direction. If you have a signed 
hypothesis, then you can run it with pos or neg instead of abs, however, 
in this case it will change the voxel-wise cluster-forming threshold 
(make it more liberal) because the voxel-wise p-value is computed 
assuming an unsigned test.

On 05/10/2016 11:59 AM, Ajay Kurani wrote:
> Hi Doug,
>Ok this makes more sense now.  In my case if I choose abs I would 
> look at the max cdf < 0.05 for the corresponding cluster extent in the 
> TH13 folder.
>
>
> In terms of the |a-b|<0,05 does this mean that if I got results in 
> blue it just means significant but with no directionality as to if A > 
> B or B>A?  I guess with the blue and red color bars I thought 
> directionality was implied.
>
> Or would one need to do a subsequent one tailed test (Pos A>B; Neg 
> B>A)d in order to determine directionality of thickness results?
>
> Thanks,
> Ajay
>
> On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness
> files (smoothed 15mm translates to FWHM=21mm), I looked at
> fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option
> mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it
> the alpha per tail (5% A>B, 5% B>A)?  Would I look at the max cdf
> 0.05 which is a cluster size of 1302 or would I look at max cdf
> <0.1 which is 1109?  This relates to the first question of if 0.05
> relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied?  I initially thought that T
> or Z=1.3 is the threshold but in looking at tutorials I see that
> may be related to the color scale -log(0.05), so I am not sure if
> there is a minimum T/Z value to be included in the cluster or if I
> was correct at 1.3 is the threshold value (T or Z score or
> something else)?.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani
> > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my
> thickness files (smoothed 15mm translates to FWHM=21mm), I
> looked at fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3
> option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A )
> or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at
> the max cdf 0.05 which is a cluster size of 1302 or would I
> look at max cdf <0.1 which is 1109?  This relates to the first
> question of if 0.05 relates to the overall probability or per
> tail.
>
> Also is there a T/Z threshold applied to these clusters or
> just cluster-extent is used?  In looking at the tutorials I
> see that 1.3 really is -log(0.05) so I do not think this
> relates to any sort of T or Z threshold but I just wanted to
> verify.
>
> Thanks,
> Ajay
>
>
> Also, when smoothed at 15mm the estimated smoothness was
> around 21mm.  When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  > wrote:
>
> Hi Doug,
>I wanted to figure out what is the minimum cluster
> extent for a given monte carlo simulation (ie when you
> choose p=0.5/T=1.3).  I saw the following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
> and so I wanted to know if freesurfer estimates the
> smoothness for each subject's cortical thickness for a
> hemisphere and then chooses the corresponding fwhm folder
> or if by choosing lh 15mm in qdec the clusterwise values
> are taken from the 15mm folder?  Is the smoothness based
> on the smoothing kernel used or the inherent smoothness of
> that particular measure (ie measuring the smoothness of
> the input thicknesss image)?  Is there a way to see what
> cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of
> cortical thickness, qcache, mris_fwhm or mri_surf2surf
> would all do the same thing and so I should be getting
> similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared
> to mri_smooth.
>
> For mri_surf2surf I used the following command for
> smoothing LGI and cortical thickness and 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Ok this makes more sense now.  In my case if I choose abs I would look
at the max cdf < 0.05 for the corresponding cluster extent in the TH13
folder.


In terms of the |a-b|<0,05 does this mean that if I got results in blue it
just means significant but with no directionality as to if A > B or B>A?  I
guess with the blue and red color bars I thought directionality was
implied.

Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in
order to determine directionality of thickness results?

Thanks,
Ajay

On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
> file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
> overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
> (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
> of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
> first question of if 0.05 relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied?  I initially thought that T or
> Z=1.3 is the threshold but in looking at tutorials I see that may be
> related to the color scale -log(0.05), so I am not sure if there is a
> minimum T/Z value to be included in the cluster or if I was correct at 1.3
> is the threshold value (T or Z score or something else)?.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the explanation. In using p=0.05 with my thickness files
>> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
>> file.
>>
>>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean
>> the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per
>> tail (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster
>> size of 1302 or would I look at max cdf <0.1 which is 1109?  This relates
>> to the first question of if 0.05 relates to the overall probability or per
>> tail.
>>
>> Also is there a T/Z threshold applied to these clusters or just
>> cluster-extent is used?  In looking at the tutorials I see that 1.3 really
>> is -log(0.05) so I do not think this relates to any sort of T or Z
>> threshold but I just wanted to verify.
>>
>> Thanks,
>> Ajay
>>
>>
>>
>> Also, when smoothed at 15mm the estimated smoothness was around 21mm.
>> When lo
>>
>>
>> On Friday, May 6, 2016, Ajay Kurani  wrote:
>>
>>> Hi Doug,
>>>I wanted to figure out what is the minimum cluster extent for a given
>>> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
>>> following tutorial :
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so
>>> I wanted to know if freesurfer estimates the smoothness for each subject's
>>> cortical thickness for a hemisphere and then chooses the corresponding fwhm
>>> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
>>> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
>>> or the inherent smoothness of that particular measure (ie measuring the
>>> smoothness of the input thicknesss image)?  Is there a way to see what
>>> cluster minimum is used?
>>>
>>> Thanks,
>>> Ajay
>>>
>>>
>>> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Doug,
Thanks for the clarification.  So in the case of cortical thickness,
 qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
 should be getting similar results if everything is entered in the same
 fashion.  This would be the approriate choice compared to mri_smooth.

 For mri_surf2surf I used the following command for smoothing LGI and
 cortical thickness and converting to .gii files.

 mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
 rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
 mris_convert -c rh.thickness.fwhm15.mgz
 $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii


 1) For cortical thickness does it make sense to use the --cortex option
 or should I specify a mask of some type (if so which) in mris_surf2surf?

 2) For converting files to .gii should I be using rh.white as the
 option or should it be rh.pial?


 Best,
 Ajay



 On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
 wrote:

> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
> analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

On 05/09/2016 04:11 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files 
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ 
> cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean 
> the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha 
> per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a 
> cluster size of 1302 or would I look at max cdf <0.1 which is 1109?  
> This relates to the first question of if 0.05 relates to the overall 
> probability or per tail.
It is the overall alpha, but the test is unsigned, so it is 5% for |A-B|>0
>
> Also is there a T/Z threshold applied?  I initially thought that T or 
> Z=1.3 is the threshold but in looking at tutorials I see that may be 
> related to the color scale -log(0.05), so I am not sure if there is a 
> minimum T/Z value to be included in the cluster or if I was correct at 
> 1.3 is the threshold value (T or Z score or something else)?.
In the simulation, the cluster-forming threshold (eg, p<.01,sig>2) is 
converted into a z-score and used to threshold the smoothed z-map. No 
t-thresholding is done,.
>
> Thanks,
> Ajay
>
> On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness
> files (smoothed 15mm translates to FWHM=21mm), I looked at
> fwhm21/abs/th13/ cdf file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option
> mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it
> the alpha per tail (5% A>B, 5% B>A)?  Would I look at the max cdf
> 0.05 which is a cluster size of 1302 or would I look at max cdf
> <0.1 which is 1109?  This relates to the first question of if 0.05
> relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied to these clusters or just
> cluster-extent is used?  In looking at the tutorials I see that
> 1.3 really is -log(0.05) so I do not think this relates to any
> sort of T or Z threshold but I just wanted to verify.
>
> Thanks,
> Ajay
>
>
> Also, when smoothed at 15mm the estimated smoothness was around
> 21mm.  When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  > wrote:
>
> Hi Doug,
>I wanted to figure out what is the minimum cluster extent
> for a given monte carlo simulation (ie when you choose
> p=0.5/T=1.3). I saw the following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
> and so I wanted to know if freesurfer estimates the smoothness
> for each subject's cortical thickness for a hemisphere and
> then chooses the corresponding fwhm folder or if by choosing
> lh 15mm in qdec the clusterwise values are taken from the 15mm
> folder?  Is the smoothness based on the smoothing kernel used
> or the inherent smoothness of that particular measure (ie
> measuring the smoothness of the input thicknesss image)?  Is
> there a way to see what cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of
> cortical thickness, qcache, mris_fwhm or mri_surf2surf
> would all do the same thing and so I should be getting
> similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared to
> mri_smooth.
>
> For mri_surf2surf I used the following command for
> smoothing LGI and cortical thickness and converting to
> .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15
> --sval rh.thickness.fsaverage.mgh --tval
> rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white
> rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the
> --cortex option or should I specify a mask of some type
> (if so which) in mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white
> as the option or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani
>  wrote:
>
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with
> mris_smooth and mri_surf2surf 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.

 In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
(5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
first question of if 0.05 relates to the overall probability or per tail.

Also is there a T/Z threshold applied?  I initially thought that T or Z=1.3
is the threshold but in looking at tutorials I see that may be related to
the color scale -log(0.05), so I am not sure if there is a minimum T/Z
value to be included in the cluster or if I was correct at 1.3 is the
threshold value (T or Z score or something else)?.

Thanks,
Ajay

On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the explanation. In using p=0.05 with my thickness files
> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
> file.
>
>  In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
> overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
> (5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
> of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
> first question of if 0.05 relates to the overall probability or per tail.
>
> Also is there a T/Z threshold applied to these clusters or just
> cluster-extent is used?  In looking at the tutorials I see that 1.3 really
> is -log(0.05) so I do not think this relates to any sort of T or Z
> threshold but I just wanted to verify.
>
> Thanks,
> Ajay
>
>
>
> Also, when smoothed at 15mm the estimated smoothness was around 21mm.
> When lo
>
>
> On Friday, May 6, 2016, Ajay Kurani  wrote:
>
>> Hi Doug,
>>I wanted to figure out what is the minimum cluster extent for a given
>> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
>> following tutorial :
>> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so
>> I wanted to know if freesurfer estimates the smoothness for each subject's
>> cortical thickness for a hemisphere and then chooses the corresponding fwhm
>> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
>> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
>> or the inherent smoothness of that particular measure (ie measuring the
>> smoothness of the input thicknesss image)?  Is there a way to see what
>> cluster minimum is used?
>>
>> Thanks,
>> Ajay
>>
>>
>> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Doug,
>>>Thanks for the clarification.  So in the case of cortical thickness,
>>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
>>> should be getting similar results if everything is entered in the same
>>> fashion.  This would be the approriate choice compared to mri_smooth.
>>>
>>> For mri_surf2surf I used the following command for smoothing LGI and
>>> cortical thickness and converting to .gii files.
>>>
>>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
>>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
>>> mris_convert -c rh.thickness.fwhm15.mgz
>>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>>>
>>>
>>> 1) For cortical thickness does it make sense to use the --cortex option
>>> or should I specify a mask of some type (if so which) in mris_surf2surf?
>>>
>>> 2) For converting files to .gii should I be using rh.white as the option
>>> or should it be rh.pial?
>>>
>>>
>>> Best,
>>> Ajay
>>>
>>>
>>>
>>> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Doug,
Thanks for the quick reply.

 Is there a difference  from qcache/mris_fwhm with mris_smooth and
 mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
 analysis?

 Thanks,
 Ajay

 On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
 wrote:

> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts which
> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
> cortical thickness analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
> group analysis.  After finding regions of difference, I would then like to
> use the ROI to extract each individual's mean thickness in the ROI in 
> order
> to run a correlation with other measures.  Based on this, I assume it 
> would
> make sense to use smoothed data to identify the ROI and then use 
> unsmoothed
> data for extracting 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the explanation. In using p=0.05 with my thickness files
(smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf
file.

 In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the
overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail
(5% A>B, 5% B>A)?  Would I look at the max cdf 0.05 which is a cluster size
of 1302 or would I look at max cdf <0.1 which is 1109?  This relates to the
first question of if 0.05 relates to the overall probability or per tail.

Also is there a T/Z threshold applied to these clusters or just
cluster-extent is used?  In looking at the tutorials I see that 1.3 really
is -log(0.05) so I do not think this relates to any sort of T or Z
threshold but I just wanted to verify.

Thanks,
Ajay



Also, when smoothed at 15mm the estimated smoothness was around 21mm.  When
lo


On Friday, May 6, 2016, Ajay Kurani  wrote:

> Hi Doug,
>I wanted to figure out what is the minimum cluster extent for a given
> monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
> following tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
> wanted to know if freesurfer estimates the smoothness for each subject's
> cortical thickness for a hemisphere and then chooses the corresponding fwhm
> folder or if by choosing lh 15mm in qdec the clusterwise values are taken
> from the 15mm folder?  Is the smoothness based on the smoothing kernel used
> or the inherent smoothness of that particular measure (ie measuring the
> smoothness of the input thicknesss image)?  Is there a way to see what
> cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the clarification.  So in the case of cortical thickness,
>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
>> should be getting similar results if everything is entered in the same
>> fashion.  This would be the approriate choice compared to mri_smooth.
>>
>> For mri_surf2surf I used the following command for smoothing LGI and
>> cortical thickness and converting to .gii files.
>>
>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
>> mris_convert -c rh.thickness.fwhm15.mgz
>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>>
>>
>> 1) For cortical thickness does it make sense to use the --cortex option
>> or should I specify a mask of some type (if so which) in mris_surf2surf?
>>
>> 2) For converting files to .gii should I be using rh.white as the option
>> or should it be rh.pial?
>>
>>
>> Best,
>> Ajay
>>
>>
>>
>> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Doug,
>>>Thanks for the quick reply.
>>>
>>> Is there a difference  from qcache/mris_fwhm with mris_smooth and
>>> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
>>> analysis?
>>>
>>> Thanks,
>>> Ajay
>>>
>>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Freesurfer Experts,
Just as a followup through my reading i've come across posts which
 use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
 cortical thickness analysis I would like to smooth all of my
 rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
 group analysis.  After finding regions of difference, I would then like to
 use the ROI to extract each individual's mean thickness in the ROI in order
 to run a correlation with other measures.  Based on this, I assume it would
 make sense to use smoothed data to identify the ROI and then use unsmoothed
 data for extracting actual thickness measures (does lh.thickness.fsaverage
 contain the original thickness or warped thickness values).

 I am unsure which smoothing is the most accurate or preferred.  In
 using qcache the smoothness of the images do not seem to reach the filter
 level (based on the earlier email) so I am not sure if there is a
 freesurfer tool to check the smoothness level or if the qcache smoothness
 levels make sense for cortical thickness.

 Thanks,
 Ajay

 On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
 wrote:

> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache option and
> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
> (converted) files.  I used an afni tool SurfFWHM to estimate the 
> smoothness
> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
> and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by 
computing the pearson correation coefficient of the residual error 
between adjacent vertices. This is then averaged over all vertices to 
compute a mean cor coef. A transform is then applied to compute the 
FWHM. This is consistent in that if you synthesize white gaussian noise 
on the surface, then smooth it with a given FWHM (mri_surf2surf or 
mris_fwhm), then use that data to compute the FWHM, the applied and 
estimated FWHM will be equal (or close).

If you look in a given file produced by the simulator, eg,
  
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th20/mc-z.cdf
the two relevant columns will be MaxClustBin and MaxClustCDF, eg,
# BinNo  MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin 
MaxSigPDF MaxSigCDF
   33  181.572128   0.010100 0.092500  0.132425 14.427808  
0.004600  0.593700
Means that a cluster of size 181.57 has a probability of 0.0925 under 
the null when the FWHM=10 and the threshold is p<.01 (th20)




On 05/06/2016 03:59 PM, Ajay Kurani wrote:
> Hi Doug,
>I wanted to figure out what is the minimum cluster extent for a 
> given monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw 
> the following tutorial : 
> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and 
> so I wanted to know if freesurfer estimates the smoothness for each 
> subject's cortical thickness for a hemisphere and then chooses the 
> corresponding fwhm folder or if by choosing lh 15mm in qdec the 
> clusterwise values are taken from the 15mm folder?  Is the smoothness 
> based on the smoothing kernel used or the inherent smoothness of that 
> particular measure (ie measuring the smoothness of the input 
> thicknesss image)?  Is there a way to see what cluster minimum is used?
>
> Thanks,
> Ajay
>
>
> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>Thanks for the clarification.  So in the case of cortical
> thickness, qcache, mris_fwhm or mri_surf2surf would all do the
> same thing and so I should be getting similar results if
> everything is entered in the same fashion. This would be the
> approriate choice compared to mri_smooth.
>
> For mri_surf2surf I used the following command for smoothing LGI
> and cortical thickness and converting to .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white
> rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the --cortex
> option or should I specify a mask of some type (if so which) in
> mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white as the
> option or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani
> > wrote:
>
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth
> and mri_surf2surf -fwhm ? If so,  which is recommended for
> cortical thickness analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani
> >
> wrote:
>
> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across
> posts which use qcache, mris_fwhm, mri_surf2surf or
> mris_smooth for smoothing.  For my cortical thickness
> analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in
> order to run a group analysis.  After finding regions of
> difference, I would then like to use the ROI to extract
> each individual's mean thickness in the ROI in order to
> run a correlation with other measures.  Based on this, I
> assume it would make sense to use smoothed data to
> identify the ROI and then use unsmoothed data for
> extracting actual thickness measures (does
> lh.thickness.fsaverage contain the original thickness or
> warped thickness values).
>
> I am unsure which smoothing is the most accurate or
> preferred.  In using qcache the smoothness of the images
> do not seem to reach the filter level (based on the
> earlier email) so I am not sure if there is a freesurfer
> tool to check the smoothness level or if the qcache
> smoothness levels make sense for cortical thickness.
>
> Thanks,
> Ajay
>
> 

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   I wanted to figure out what is the minimum cluster extent for a given
monte carlo simulation (ie when you choose p=0.5/T=1.3).  I saw the
following tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I
wanted to know if freesurfer estimates the smoothness for each subject's
cortical thickness for a hemisphere and then chooses the corresponding fwhm
folder or if by choosing lh 15mm in qdec the clusterwise values are taken
from the 15mm folder?  Is the smoothness based on the smoothing kernel used
or the inherent smoothness of that particular measure (ie measuring the
smoothness of the input thicknesss image)?  Is there a way to see what
cluster minimum is used?

Thanks,
Ajay


On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the clarification.  So in the case of cortical thickness,
> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
> should be getting similar results if everything is entered in the same
> fashion.  This would be the approriate choice compared to mri_smooth.
>
> For mri_surf2surf I used the following command for smoothing LGI and
> cortical thickness and converting to .gii files.
>
> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
> mris_convert -c rh.thickness.fwhm15.mgz
> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
>
>
> 1) For cortical thickness does it make sense to use the --cortex option or
> should I specify a mask of some type (if so which) in mris_surf2surf?
>
> 2) For converting files to .gii should I be using rh.white as the option
> or should it be rh.pial?
>
>
> Best,
> Ajay
>
>
>
> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
> wrote:
>
>> Hi Doug,
>>Thanks for the quick reply.
>>
>> Is there a difference  from qcache/mris_fwhm with mris_smooth and
>> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
>> analysis?
>>
>> Thanks,
>> Ajay
>>
>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Freesurfer Experts,
>>>Just as a followup through my reading i've come across posts which
>>> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
>>> cortical thickness analysis I would like to smooth all of my
>>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
>>> group analysis.  After finding regions of difference, I would then like to
>>> use the ROI to extract each individual's mean thickness in the ROI in order
>>> to run a correlation with other measures.  Based on this, I assume it would
>>> make sense to use smoothed data to identify the ROI and then use unsmoothed
>>> data for extracting actual thickness measures (does lh.thickness.fsaverage
>>> contain the original thickness or warped thickness values).
>>>
>>> I am unsure which smoothing is the most accurate or preferred.  In using
>>> qcache the smoothness of the images do not seem to reach the filter level
>>> (based on the earlier email) so I am not sure if there is a freesurfer tool
>>> to check the smoothness level or if the qcache smoothness levels make sense
>>> for cortical thickness.
>>>
>>> Thanks,
>>> Ajay
>>>
>>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
>>> wrote:
>>>
 Hi Freesurfer Experts,
I am trying to understand the difference between qcache option and
 mris_fwhm and which is appropriate for a cortical thickness analysis.  I
 processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
 (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
 of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
 and 20mm it was approximately 9.3-9.9 smoothness level.

 I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
 lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
 using SurfFWHM on the smae subject the smoothness was estimated at 11.25.


 1) I am not sure if the qcache or the mris_fwhm file is more
 appropriate to use for a cortical thickness analysis.

 2) For qdec if I select the 15mm  option does it assume the smoothness
 is 15mm when calculating monte carlo corrections?  Would there be a
 different way to estimate this since my smoothness at 15mm is closer to
 10mm?

 Thanks,
 Ajay

>>>
>>>
>>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the clarification.  So in the case of cortical thickness,
qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I
should be getting similar results if everything is entered in the same
fashion.  This would be the approriate choice compared to mri_smooth.

For mri_surf2surf I used the following command for smoothing LGI and
cortical thickness and converting to .gii files.

mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval
rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex
mris_convert -c rh.thickness.fwhm15.mgz
$FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii


1) For cortical thickness does it make sense to use the --cortex option or
should I specify a mask of some type (if so which) in mris_surf2surf?

2) For converting files to .gii should I be using rh.white as the option or
should it be rh.pial?


Best,
Ajay



On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani 
wrote:

> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
> analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>Just as a followup through my reading i've come across posts which use
>> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
>> cortical thickness analysis I would like to smooth all of my
>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
>> group analysis.  After finding regions of difference, I would then like to
>> use the ROI to extract each individual's mean thickness in the ROI in order
>> to run a correlation with other measures.  Based on this, I assume it would
>> make sense to use smoothed data to identify the ROI and then use unsmoothed
>> data for extracting actual thickness measures (does lh.thickness.fsaverage
>> contain the original thickness or warped thickness values).
>>
>> I am unsure which smoothing is the most accurate or preferred.  In using
>> qcache the smoothness of the images do not seem to reach the filter level
>> (based on the earlier email) so I am not sure if there is a freesurfer tool
>> to check the smoothness level or if the qcache smoothness levels make sense
>> for cortical thickness.
>>
>> Thanks,
>> Ajay
>>
>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
>> wrote:
>>
>>> Hi Freesurfer Experts,
>>>I am trying to understand the difference between qcache option and
>>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>>
>>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>>
>>>
>>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>>> to use for a cortical thickness analysis.
>>>
>>> 2) For qdec if I select the 15mm  option does it assume the smoothness
>>> is 15mm when calculating monte carlo corrections?  Would there be a
>>> different way to estimate this since my smoothness at 15mm is closer to
>>> 10mm?
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas N Greve]

There is not a difference between mris_fwhm and mri_surf2surf. 
mris_smooth smoothes the xyz coordinates of the vertices of a surface 
(the others smooth an overlay).

On 05/05/2016 03:53 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the quick reply.
>
> Is there a difference  from qcache/mris_fwhm with mris_smooth and 
> mri_surf2surf -fwhm ?  If so,  which is recommended for cortical 
> thickness analysis?
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani  > wrote:
>
> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts
> which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for
> smoothing.  For my cortical thickness analysis I would like to
> smooth all of my rh/lh.thickness.fsaverage.mgh files for each
> subject in order to run a group analysis.  After finding regions
> of difference, I would then like to use the ROI to extract each
> individual's mean thickness in the ROI in order to run a
> correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use
> unsmoothed data for extracting actual thickness measures (does
> lh.thickness.fsaverage contain the original thickness or warped
> thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In
> using qcache the smoothness of the images do not seem to reach the
> filter level (based on the earlier email) so I am not sure if
> there is a freesurfer tool to check the smoothness level or if the
> qcache smoothness levels make sense for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani
> > wrote:
>
> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache
> option and mris_fwhm and which is appropriate for a cortical
> thickness analysis.  I processed my  files with qcache and
> have lh.thickness.fsaverage.fwhm15.gii (converted) files.  I
> used an afni tool SurfFWHM to estimate the smoothness of a
> subject at when looking at the fwhm0 image it iwas 5.5 and for
> 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only
> --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o
> test_15.gii  and when using SurfFWHM on the smae subject the
> smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more
> appropriate to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the
> smoothness is 15mm when calculating monte carlo corrections? 
> Would there be a different way to estimate this since my
> smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Doug,
   Thanks for the quick reply.

Is there a difference  from qcache/mris_fwhm with mris_smooth and
mri_surf2surf -fwhm ?  If so,  which is recommended for cortical thickness
analysis?

Thanks,
Ajay

On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>Just as a followup through my reading i've come across posts which use
> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
> cortical thickness analysis I would like to smooth all of my
> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
> group analysis.  After finding regions of difference, I would then like to
> use the ROI to extract each individual's mean thickness in the ROI in order
> to run a correlation with other measures.  Based on this, I assume it would
> make sense to use smoothed data to identify the ROI and then use unsmoothed
> data for extracting actual thickness measures (does lh.thickness.fsaverage
> contain the original thickness or warped thickness values).
>
> I am unsure which smoothing is the most accurate or preferred.  In using
> qcache the smoothness of the images do not seem to reach the filter level
> (based on the earlier email) so I am not sure if there is a freesurfer tool
> to check the smoothness level or if the qcache smoothness levels make sense
> for cortical thickness.
>
> Thanks,
> Ajay
>
> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>I am trying to understand the difference between qcache option and
>> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
>> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
>> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
>> and 20mm it was approximately 9.3-9.9 smoothness level.
>>
>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>>
>>
>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
>> to use for a cortical thickness analysis.
>>
>> 2) For qdec if I select the 15mm  option does it assume the smoothness is
>> 15mm when calculating monte carlo corrections?  Would there be a different
>> way to estimate this since my smoothness at 15mm is closer to 10mm?
>>
>> Thanks,
>> Ajay
>>
>
>
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Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Douglas Greve]

Underneath, they both use the same code, so they should give the same 
results. Are you saying they are different? I don't know what SurfFWHM 
is doing so I can't comment on what those results mean. Measuring the 
FWHM on the surface is quite tricky.

doug


On 5/4/16 6:41 PM, Ajay Kurani wrote:

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and 
mris_fwhm and which is appropriate for a cortical thickness analysis.  
I processed my  files with qcache and have 
lh.thickness.fsaverage.fwhm15.gii (converted) files.  I used an afni 
tool SurfFWHM to estimate the smoothness of a subject at when looking 
at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was 
approximately 9.3-9.9 smoothness level.


I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i 
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and 
when using SurfFWHM on the smae subject the smoothness was estimated 
at 11.25.



1) I am not sure if the qcache or the mris_fwhm file is more 
appropriate to use for a cortical thickness analysis.


2) For qdec if I select the 15mm  option does it assume the smoothness 
is 15mm when calculating monte carlo corrections?  Would there be a 
different way to estimate this since my smoothness at 15mm is closer 
to 10mm?


Thanks,
Ajay


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   Just as a followup through my reading i've come across posts which use
qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing.  For my
cortical thickness analysis I would like to smooth all of my
rh/lh.thickness.fsaverage.mgh files for each subject in order to run a
group analysis.  After finding regions of difference, I would then like to
use the ROI to extract each individual's mean thickness in the ROI in order
to run a correlation with other measures.  Based on this, I assume it would
make sense to use smoothed data to identify the ROI and then use unsmoothed
data for extracting actual thickness measures (does lh.thickness.fsaverage
contain the original thickness or warped thickness values).

I am unsure which smoothing is the most accurate or preferred.  In using
qcache the smoothness of the images do not seem to reach the filter level
(based on the earlier email) so I am not sure if there is a freesurfer tool
to check the smoothness level or if the qcache smoothness levels make sense
for cortical thickness.

Thanks,
Ajay

On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani 
wrote:

> Hi Freesurfer Experts,
>I am trying to understand the difference between qcache option and
> mris_fwhm and which is appropriate for a cortical thickness analysis.  I
> processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
> (converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
> and 20mm it was approximately 9.3-9.9 smoothness level.
>
> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
> using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
>
>
> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate
> to use for a cortical thickness analysis.
>
> 2) For qdec if I select the 15mm  option does it assume the smoothness is
> 15mm when calculating monte carlo corrections?  Would there be a different
> way to estimate this since my smoothness at 15mm is closer to 10mm?
>
> Thanks,
> Ajay
>
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[Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

[Ajay Kurani]

Hi Freesurfer Experts,
   I am trying to understand the difference between qcache option and
mris_fwhm and which is appropriate for a cortical thickness analysis.  I
processed my  files with qcache and have lh.thickness.fsaverage.fwhm15.gii
(converted) files.  I used an afni tool SurfFWHM to estimate the smoothness
of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15
and 20mm it was approximately 9.3-9.9 smoothness level.

I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i
lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii  and when
using SurfFWHM on the smae subject the smoothness was estimated at 11.25.


1) I am not sure if the qcache or the mris_fwhm file is more appropriate to
use for a cortical thickness analysis.

2) For qdec if I select the 15mm  option does it assume the smoothness is
15mm when calculating monte carlo corrections?  Would there be a different
way to estimate this since my smoothness at 15mm is closer to 10mm?

Thanks,
Ajay
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